@haniffalab/cherita-react 1.3.0 → 1.3.1-dev.2025-10-29.6de4119f

package/dist/cjs/constants/colorscales.js

@@ -6,23 +6,23 @@ Object.defineProperty(exports, "__esModule", {
 exports.COLORSCALES = void 0;
 // From plotly https://github.com/plotly/plotly.js/blob/5bc25b490702e5ed61265207833dbd58e8ab27f1/src/components/colorscale/scales.js
 const COLORSCALES = exports.COLORSCALES = {
-  Greys: ["#000000", "#ffffff"],
-  YlGnBu: ["#081d58", "#253494", "#225ea8", "#1d91c0", "#41b6c4", "#7fcdbb", "#c7e9b4", "#edf8d9", "#ffffd9"],
-  Greens: ["#00441b", "#006d2c", "#238b45", "#41ab5d", "#74c476", "#a1d9a5", "#c7e9c0", "#e5f5e0", "#f7fcf5"],
-  YlOrRd: ["#800026", "#bd0026", "#e31a1c", "#fc4e2a", "#fd8d3c", "#feb24c", "#fed976", "#ffed9f", "#ffffcc"],
-  Bluered: ["#0000ff", "#ff0000"],
-  RdBu: ["#050aac", "#6a89f7", "#bebebe", "#dcaa84", "#e6915a", "#b20a1c"],
-  Reds: ["#dcdcdc", "#f5c39d", "#f5a069", "#b20a1c"],
-  Blues: ["#050aac", "#283cba", "#4664f5", "#5a78f5", "#6a89f7", "#dcdcdc"],
-  Picnic: ["#0000ff", "#3399ff", "#66ccff", "#99ccff", "#ccccff", "#ffffff", "#ffccff", "#ff99ff", "#ff66cc", "#ff6666", "#ff0000"],
-  Rainbow: ["#96005a", "#0000c8", "#0019ff", "#0098ff", "#2cff96", "#97ff00", "#ffe600", "#ff6f00", "#ff0000"],
-  Portland: ["#0c3383", "#0a88ba", "#f2d338", "#f28f38", "#d91e1e"],
-  Jet: ["#000083", "#003caa", "#05ffff", "#ffff00", "#fa0000", "#800000"],
-  Hot: ["#000000", "#e60000", "#ffd200", "#ffffff"],
-  Blackbody: ["#000000", "#e60000", "#e6d200", "#ffffff", "#a0c8ff"],
-  Earth: ["#000082", "#00b4b4", "#28d228", "#e6e632", "#784614", "#ffffff"],
-  Electric: ["#000000", "#1e0064", "#780064", "#a05a00", "#e6c800", "#fffadc"],
-  Viridis: ["#440154", "#48186a", "#472d7b", "#424086", "#3b528b", "#33638d", "#2c728e", "#26828e", "#21918c", "#1fa088", "#28ae80", "#3fbc73", "#5ec962", "#84d44b", "#addc30", "#d8e219", "#fde725"],
-  Cividis: ["#00204c", "#002a66", "#00346e", "#273f6c", "#3c4a6c", "#4c556b", "#5b5f6d", "#686a70", "#757575", "#838178", "#929c78", "#a19676", "#b0a572", "#c0af6d", "#d1ba65", "#e1c75c", "#f3db4f", "#ffe945"],
-  Accent: ["#7fc97f", "#beaed4", "#fdc086", "#ffff99", "#386cb0", "#f0027f", "#bf5b17", "#666666"]
+  Greys: ['#000000', '#ffffff'],
+  YlGnBu: ['#081d58', '#253494', '#225ea8', '#1d91c0', '#41b6c4', '#7fcdbb', '#c7e9b4', '#edf8d9', '#ffffd9'],
+  Greens: ['#00441b', '#006d2c', '#238b45', '#41ab5d', '#74c476', '#a1d9a5', '#c7e9c0', '#e5f5e0', '#f7fcf5'],
+  YlOrRd: ['#800026', '#bd0026', '#e31a1c', '#fc4e2a', '#fd8d3c', '#feb24c', '#fed976', '#ffed9f', '#ffffcc'],
+  Bluered: ['#0000ff', '#ff0000'],
+  RdBu: ['#050aac', '#6a89f7', '#bebebe', '#dcaa84', '#e6915a', '#b20a1c'],
+  Reds: ['#dcdcdc', '#f5c39d', '#f5a069', '#b20a1c'],
+  Blues: ['#050aac', '#283cba', '#4664f5', '#5a78f5', '#6a89f7', '#dcdcdc'],
+  Picnic: ['#0000ff', '#3399ff', '#66ccff', '#99ccff', '#ccccff', '#ffffff', '#ffccff', '#ff99ff', '#ff66cc', '#ff6666', '#ff0000'],
+  Rainbow: ['#96005a', '#0000c8', '#0019ff', '#0098ff', '#2cff96', '#97ff00', '#ffe600', '#ff6f00', '#ff0000'],
+  Portland: ['#0c3383', '#0a88ba', '#f2d338', '#f28f38', '#d91e1e'],
+  Jet: ['#000083', '#003caa', '#05ffff', '#ffff00', '#fa0000', '#800000'],
+  Hot: ['#000000', '#e60000', '#ffd200', '#ffffff'],
+  Blackbody: ['#000000', '#e60000', '#e6d200', '#ffffff', '#a0c8ff'],
+  Earth: ['#000082', '#00b4b4', '#28d228', '#e6e632', '#784614', '#ffffff'],
+  Electric: ['#000000', '#1e0064', '#780064', '#a05a00', '#e6c800', '#fffadc'],
+  Viridis: ['#440154', '#48186a', '#472d7b', '#424086', '#3b528b', '#33638d', '#2c728e', '#26828e', '#21918c', '#1fa088', '#28ae80', '#3fbc73', '#5ec962', '#84d44b', '#addc30', '#d8e219', '#fde725'],
+  Cividis: ['#00204c', '#002a66', '#00346e', '#273f6c', '#3c4a6c', '#4c556b', '#5b5f6d', '#686a70', '#757575', '#838178', '#929c78', '#a19676', '#b0a572', '#c0af6d', '#d1ba65', '#e1c75c', '#f3db4f', '#ffe945'],
+  Accent: ['#7fc97f', '#beaed4', '#fdc086', '#ffff99', '#386cb0', '#f0027f', '#bf5b17', '#666666']
 };

package/dist/cjs/constants/constants.js

@@ -3,92 +3,107 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.VIOLIN_MODES = exports.VIOLINPLOT_SCALES = exports.VAR_SORT_ORDER = exports.VAR_SORT = exports.UNSELECTED_POLYGON_FILLCOLOR = exports.SELECTION_MODES = exports.SELECTED_POLYGON_FILLCOLOR = exports.PSEUDOSPATIAL_PLOT_TYPES = exports.PSEUDOSPATIAL_CATEGORICAL_MODES = exports.OBS_TYPES = exports.MATRIXPLOT_SCALES = exports.LOCAL_STORAGE_KEY = exports.DOTPLOT_SCALES = exports.DEFAULT_OBS_GROUP = exports.COLOR_ENCODINGS = void 0;
-const LOCAL_STORAGE_KEY = exports.LOCAL_STORAGE_KEY = "CHERITA";
+exports.VIOLIN_MODES = exports.VIOLINPLOT_SCALES = exports.VAR_SORT_ORDER = exports.VAR_SORT = exports.UNSELECTED_POLYGON_FILLCOLOR = exports.SELECTION_MODES = exports.SELECTED_POLYGON_FILLCOLOR = exports.PSEUDOSPATIAL_PLOT_TYPES = exports.PSEUDOSPATIAL_CATEGORICAL_MODES = exports.PLOT_TYPES = exports.PLOTLY_MODEBAR_BUTTONS = exports.OBS_TYPES = exports.MATRIXPLOT_SCALES = exports.LOCAL_STORAGE_KEY = exports.DOTPLOT_SCALES = exports.DEFAULT_OBS_GROUP = exports.DEFAULT_OBSM_KEYS = exports.COLOR_ENCODINGS = exports.BREAKPOINTS = void 0;
+const LOCAL_STORAGE_KEY = exports.LOCAL_STORAGE_KEY = 'CHERITA';
+const PLOT_TYPES = exports.PLOT_TYPES = {
+  SCATTERPLOT: 'scatterplot',
+  DOTPLOT: 'dotplot',
+  HEATMAP: 'heatmap',
+  MATRIXPLOT: 'matrixplot',
+  VIOLINPLOT: 'violinplot'
+};
 const COLOR_ENCODINGS = exports.COLOR_ENCODINGS = {
-  VAR: "var",
-  OBS: "obs"
+  VAR: 'var',
+  OBS: 'obs'
 };
 const OBS_TYPES = exports.OBS_TYPES = {
-  CATEGORICAL: "categorical",
-  DISCRETE: "discrete",
-  CONTINUOUS: "continuous",
-  BOOLEAN: "boolean"
+  CATEGORICAL: 'categorical',
+  DISCRETE: 'discrete',
+  CONTINUOUS: 'continuous',
+  BOOLEAN: 'boolean'
 };
 const VAR_SORT = exports.VAR_SORT = {
   NONE: null,
-  NAME: "name",
-  MATRIX: "matrix"
+  NAME: 'name',
+  MATRIX: 'matrix'
 };
 const VAR_SORT_ORDER = exports.VAR_SORT_ORDER = {
-  ASC: "asc",
-  DESC: "desc"
+  ASC: 'asc',
+  DESC: 'desc'
 };
 const SELECTED_POLYGON_FILLCOLOR = exports.SELECTED_POLYGON_FILLCOLOR = [107, 170, 209, 255 / 2];
 const UNSELECTED_POLYGON_FILLCOLOR = exports.UNSELECTED_POLYGON_FILLCOLOR = [167, 191, 211, 255 / 3];
 const SELECTION_MODES = exports.SELECTION_MODES = {
-  SINGLE: "single",
-  MULTIPLE: "multiple"
+  SINGLE: 'single',
+  MULTIPLE: 'multiple'
 };
 const VIOLIN_MODES = exports.VIOLIN_MODES = {
-  MULTIKEY: "multikey",
-  GROUPBY: "groupby"
+  MULTIKEY: 'multikey',
+  GROUPBY: 'groupby'
 };
 const MATRIXPLOT_SCALES = exports.MATRIXPLOT_SCALES = {
   NONE: {
     value: null,
-    name: "None"
+    name: 'None'
   },
   GROUP: {
-    value: "group",
-    name: "Group"
+    value: 'group',
+    name: 'Group'
   },
   VAR: {
-    value: "var",
-    name: "Var"
+    value: 'var',
+    name: 'Var'
   }
 };
 const DOTPLOT_SCALES = exports.DOTPLOT_SCALES = {
   NONE: {
     value: null,
-    name: "None"
+    name: 'None'
   },
   GROUP: {
-    value: "group",
-    name: "Group"
+    value: 'group',
+    name: 'Group'
   },
   VAR: {
-    value: "var",
-    name: "Var"
+    value: 'var',
+    name: 'Var'
   }
 };
 const VIOLINPLOT_SCALES = exports.VIOLINPLOT_SCALES = {
   WIDTH: {
-    value: "width",
-    name: "Width"
+    value: 'width',
+    name: 'Width'
   },
   COUNT: {
-    value: "count",
-    name: "Count"
+    value: 'count',
+    name: 'Count'
   }
 };
 const PSEUDOSPATIAL_PLOT_TYPES = exports.PSEUDOSPATIAL_PLOT_TYPES = {
-  GENE: "gene",
-  CATEGORICAL: "categorical",
-  CONTINUOUS: "continuous",
-  MASKS: "masks"
+  GENE: 'gene',
+  CATEGORICAL: 'categorical',
+  CONTINUOUS: 'continuous',
+  MASKS: 'masks'
 };
 const PSEUDOSPATIAL_CATEGORICAL_MODES = exports.PSEUDOSPATIAL_CATEGORICAL_MODES = {
   ACROSS: {
-    value: "across",
-    name: "% across sections"
+    value: 'across',
+    name: '% across sections'
   },
   WITHIN: {
-    value: "within",
-    name: "% within section"
+    value: 'within',
+    name: '% within section'
   }
 };
 
 // `default` cols to be shown out of accordion, at top of obslist
 // default values from cellxgene schema
-const DEFAULT_OBS_GROUP = exports.DEFAULT_OBS_GROUP = ["assay", "cell_type", "development_stage", "disease", "donor_id", "organism", "self_reported_ethnicity", "sex", "suspension_type", "tissue", "tissue_type"];
+const DEFAULT_OBS_GROUP = exports.DEFAULT_OBS_GROUP = ['assay', 'cell_type', 'development_stage', 'disease', 'donor_id', 'organism', 'self_reported_ethnicity', 'sex', 'suspension_type', 'tissue', 'tissue_type'];
+const PLOTLY_MODEBAR_BUTTONS = exports.PLOTLY_MODEBAR_BUTTONS = ['toImage', 'zoom2d', 'pan2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d'];
+const BREAKPOINTS = exports.BREAKPOINTS = {
+  LG: '(max-width: 991.98px)',
+  XL: '(max-width: 1199.98px)'
+};
+
+// In order of priority
+const DEFAULT_OBSM_KEYS = exports.DEFAULT_OBSM_KEYS = ['x_umap', 'x_tsne', 'x_scvi', 'x_pca'];

package/dist/cjs/context/DatasetContext.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", {
 exports.DatasetContext = void 0;
 exports.DatasetProvider = DatasetProvider;
 exports.useDataset = useDataset;
-var _react = _interopRequireWildcard(require("react"));
+var _react = require("react");
 var _querySyncStoragePersister = require("@tanstack/query-sync-storage-persister");
 var _reactQuery = require("@tanstack/react-query");
 var _reactQueryPersistClient = require("@tanstack/react-query-persist-client");
@@ -14,9 +14,9 @@ var _lodash = _interopRequireDefault(require("lodash"));
 var _FilterContext = require("./FilterContext");
 var _SettingsContext = require("./SettingsContext");
 var _ZarrDataContext = require("./ZarrDataContext");
+var _jsxRuntime = require("react/jsx-runtime");
 const _excluded = ["dataset_url", "children"];
 function _interopRequireDefault(e) { return e && e.__esModule ? e : { default: e }; }
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
 function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
@@ -43,7 +43,7 @@ const queryClient = new _reactQuery.QueryClient({
   })
 });
 // Type of queries to store responses
-const persistKeys = ["obs/cols", "var/names", "obsm/keys", "obs/bins", "obs/distribution"];
+const persistKeys = ['obs/cols', 'var/names', 'obsm/keys', 'obs/bins', 'obs/distribution'];
 const persistOptions = {
   persister: (0, _querySyncStoragePersister.createSyncStoragePersister)({
     storage: window.localStorage
@@ -54,13 +54,14 @@ const persistOptions = {
         queryKey,
         state
       } = _ref;
-      if (state.status === "success") {
+      if (state.status === 'success') {
         return persistKeys.includes(queryKey === null || queryKey === void 0 ? void 0 : queryKey[0]);
       }
       return false;
     }
-  }
-  // @TODO: add maxAge and buster (app and api version numbers as busters)
+  },
+  buster: "1.3.1-dev.2025-10-29.6de4119f" || '0.0.0'
+  // @TODO: add maxAge and api version numbers as buster
 };
 const initialDataset = {
   url: null,
@@ -69,7 +70,9 @@ const initialDataset = {
   obsGroups: null,
   imageUrl: null,
   defaultSettings: {},
-  canOverrideSettings: true
+  canOverrideSettings: true,
+  useUnsColors: false,
+  isPseudospatial: false
 };
 function DatasetProvider(_ref2) {
   let {
@@ -80,16 +83,23 @@ function DatasetProvider(_ref2) {
   const dataset = _lodash.default.assign(initialDataset, _objectSpread({
     url: dataset_url
   }, dataset_params));
-  return /*#__PURE__*/_react.default.createElement(DatasetContext.Provider, {
-    value: dataset
-  }, /*#__PURE__*/_react.default.createElement(_SettingsContext.SettingsProvider, {
-    dataset_url: dataset.url,
-    defaultSettings: dataset.defaultSettings,
-    canOverrideSettings: dataset.canOverrideSettings
-  }, /*#__PURE__*/_react.default.createElement(_reactQueryPersistClient.PersistQueryClientProvider, {
-    client: queryClient,
-    persistOptions: persistOptions
-  }, /*#__PURE__*/_react.default.createElement(_FilterContext.FilterProvider, null, /*#__PURE__*/_react.default.createElement(_ZarrDataContext.ZarrDataProvider, null, children)))));
+  return /*#__PURE__*/(0, _jsxRuntime.jsx)(DatasetContext.Provider, {
+    value: dataset,
+    children: /*#__PURE__*/(0, _jsxRuntime.jsx)(_reactQueryPersistClient.PersistQueryClientProvider, {
+      client: queryClient,
+      persistOptions: persistOptions,
+      children: /*#__PURE__*/(0, _jsxRuntime.jsx)(_SettingsContext.SettingsProvider, {
+        dataset_url: dataset.url,
+        defaultSettings: dataset.defaultSettings,
+        canOverrideSettings: dataset.canOverrideSettings,
+        children: /*#__PURE__*/(0, _jsxRuntime.jsx)(_FilterContext.FilterProvider, {
+          children: /*#__PURE__*/(0, _jsxRuntime.jsx)(_ZarrDataContext.ZarrDataProvider, {
+            children: children
+          })
+        })
+      })
+    })
+  });
 }
 function useDataset() {
   return (0, _react.useContext)(DatasetContext);

package/dist/cjs/context/FilterContext.js

@@ -7,8 +7,8 @@ exports.FilterProvider = FilterProvider;
 exports.FilteredDataDispatchContext = exports.FilteredDataContext = void 0;
 exports.useFilteredData = useFilteredData;
 exports.useFilteredDataDispatch = useFilteredDataDispatch;
-var _react = _interopRequireWildcard(require("react"));
-function _interopRequireWildcard(e, t) { if ("function" == typeof WeakMap) var r = new WeakMap(), n = new WeakMap(); return (_interopRequireWildcard = function (e, t) { if (!t && e && e.__esModule) return e; var o, i, f = { __proto__: null, default: e }; if (null === e || "object" != typeof e && "function" != typeof e) return f; if (o = t ? n : r) { if (o.has(e)) return o.get(e); o.set(e, f); } for (const t in e) "default" !== t && {}.hasOwnProperty.call(e, t) && ((i = (o = Object.defineProperty) && Object.getOwnPropertyDescriptor(e, t)) && (i.get || i.set) ? o(f, t, i) : f[t] = e[t]); return f; })(e, t); }
+var _react = require("react");
+var _jsxRuntime = require("react/jsx-runtime");
 function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty(e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 function _defineProperty(e, r, t) { return (r = _toPropertyKey(r)) in e ? Object.defineProperty(e, r, { value: t, enumerable: !0, configurable: !0, writable: !0 }) : e[r] = t, e; }
@@ -28,11 +28,13 @@ function FilterProvider(_ref) {
     children
   } = _ref;
   const [filteredData, dispatch] = (0, _react.useReducer)(filterReducer, _objectSpread({}, initialFilterData));
-  return /*#__PURE__*/_react.default.createElement(FilteredDataContext.Provider, {
-    value: filteredData
-  }, /*#__PURE__*/_react.default.createElement(FilteredDataDispatchContext.Provider, {
-    value: dispatch
-  }, children));
+  return /*#__PURE__*/(0, _jsxRuntime.jsx)(FilteredDataContext.Provider, {
+    value: filteredData,
+    children: /*#__PURE__*/(0, _jsxRuntime.jsx)(FilteredDataDispatchContext.Provider, {
+      value: dispatch,
+      children: children
+    })
+  });
 }
 function useFilteredData() {
   return (0, _react.useContext)(FilteredDataContext);
@@ -42,7 +44,7 @@ function useFilteredDataDispatch() {
 }
 function filterReducer(filteredData, action) {
   switch (action.type) {
-    case "set.obs.indices":
+    case 'set.obs.indices':
       {
         return _objectSpread(_objectSpread({}, filteredData), {}, {
           obsIndices: action.indices,
@@ -54,7 +56,7 @@ function filterReducer(filteredData, action) {
       }
     default:
       {
-        throw Error("Unknown action: " + action.type);
+        throw Error('Unknown action: ' + action.type);
       }
   }
 }